Bowen became the chief secretary to the government of the Ionian Islands in 1854.[2] While in that post, he married the Contessa Diamantina di Roma on 28 April 1856. Diamantina was the daughter of Conte Giorgio-Candiano Roma and his wife Contessa Orsola, née di Balsamo. The Roma family were local aristocracy; her father being the President of the Ionian Senate, titular head of the Islands, from 1850 to 1856. He was appointee a Companion of the Order of St Michael and St George (CMG) in 1855 and was advanced to Knight Commander (KCMG) in the following year.[3]

In 1859, Bowen was appointed the first Governor of Queensland, a colony that had just been separated from New South Wales. Bowen's influence in Queensland was greater than that of the governors in other Australian colonies in a large part due to Robert Herbert, who accompanied Bowen from England, and later became colonial secretary and then first Premier of Queensland in 1860–66.[1] Bowen was interested in the exploration of Queensland and in the establishment of a volunteer force, but incurred some unpopularity by refusing to sanction the issue of inconvertible paper money during the financial crisis of 1866. But overall, he was quite popular in Queensland, so that the citizens requested an extension of his five-year term as governor, resulting in his staying for further two years.[4]

In March 1873 Bowen was transferred to Victoria (Australia) as Governor of Victoria,[1] where he embarked on an endeavour to reduce the expenses of the colony. A political crisis while Bowen took leave in England from January 1875 to January 1876, when acting governor, Sir William Stawell, showed 'too little flexibility in the exercise of his temporary powers'.[1] One of the main issues was the conflict between the Victorian Legislative Council and the Victorian Legislative Assembly; the Council was blocking legislation for its reform and for payment of members.[1] Backed by advice from the Colonial Office, Bowen consented to Premier Graham Berry's plan to break the deadlock by wholesale dismissal of public servants on the so-called 'Black Wednesday'.[1] In May 1878 Bowen said that "my reluctant consent, purely on constitutional grounds, to these dismissals … has damaged my further reputation and my career to a degree that I shall never recover. It will never be forgotten either in England or in the Colony". However several others including Hugh Childers and William Ewart Gladstone approved of Bowen's actions.[1]

On 30 March 1883, Bowen was made Governor of Hong Kong. During his tenure, his administration established the Hong Kong Observatory, which also served as the meteorological institute of the territory. He founded the first college in Hong Kong, and ordered the construction of the Typhoon Shelter in Causeway Bay, and a government hospital. He retired in 1887, due to ill health.[7]

Bowen returned to England after his time in Hong Kong and was appointed chief of a Royal Commission sent to Malta in December 1887 to help to draft the new constitution for the island. All recommendations made by the commission were adopted. Afterwards, Bowen was sworn of the Privy Council.

George married his second wife, Letitia Florence White, in late 1896 at Chelsea, London.[8] Florence was the daughter of Dr Thomas Luby, a mathematician, and was the widow of Henry White, whom she married in 1878.[8]

George Ferguson Bowen died on 21 February 1899 in Brighton in Sussex, aged 77 years old.[8] He died from bronchitis after a short illness of 2 days. He was buried on 25 February 1899 in Kensal Green cemetery in London.